ó ¨™xTc@ sèddlmZddlmZddlmZddlZddlZddlm Z ddl m Z ddl m Z ddl mZmZdd lmZddlZddlZd Zejjd ƒZd efd „ƒYZdS(iÿÿÿÿ(tdivision(toutlier_rejection(tabsolute_scalingN(tflex(tmiller(tadptbx(tSorrytnull_out(tAutos~ hklout = None .type = path hklout_type=mtz sca *Auto .type = choice label_extension="massaged" .type = str sÉ aniso .help="Parameters dealing with anisotropy correction" .short_caption = Anisotropy correction .style = box auto_align { action=*remove_aniso None .type=choice .caption = Remove_anisotropy None .help="Remove anisotropy?" .style = bold final_b=*eigen_min eigen_mean user_b_iso .help="Final b value" .type=choice .caption = Minimum_eigenvalue Mean_eigenvalue User_specified .short_caption = Final B-factor source b_iso=None .type=float .help="User specified B value" .short_caption = User-specified B-factor } outlier .help="Outlier analyses" .short_caption = Outlier analyses .style = box auto_align { action=*extreme basic beamstop None .help="Outlier protocol" .type=choice .short_caption = Outlier rejection protocol parameters .help="Parameters for outlier detection" { basic_wilson{ level = 1E-6 .type=float .short_caption = Basic Wilson level } extreme_wilson{ level = 0.01 .type=float .short_caption = Extreme Wilson level } beamstop{ level = 0.001 .type=float .short_caption = Beamstop level d_min = 10.0 .type=float .short_caption = Max. resolution .style = resolution } } } symmetry .short_caption = Detwinning .style = box auto_align { action = detwin twin *None .type = choice .short_caption = Action .style = bold twinning_parameters{ twin_law = None .type = str .short_caption = Twin law .input_size = 120 .style = bold fraction = None .type = float .short_caption = Detwinning fraction .style = bold } } t massage_datacB s2eZdddd„Zd„Zedd„ZRS(idicC sY||_|jƒj|ƒjƒjƒ|_||_|jdkrTtj |_n|jdkrrt ƒ|_n|j|_ |jj j dkrtjd|jd|d|ƒ}d|_|jd|ƒ|j|_|j|_|j|_|jj jdkr|jd }nr|jj jd kr@tj|jƒ}nH|jj jd kr‚|jj jdk spt‚|jj j}nd }| | | dddg}tj|jƒtj |ƒƒ} tj!|jd |jƒ|_ tj!|j d | ƒ|_ |j j|ƒ|_ nt"j#|j dd|jƒ} |j |_$|jj%j dkr¡|jdIJ|jdIJ| j&d|jj%j'j(j)dt*ƒ} | |_$n|jj%j dkr|jdIJ|jdIJ| j+d|jj%j'j,j)dt*ƒ} | |_$n|jj%j dkrz|jdIJ|jdIJ| j-d|jj%j'j.j)d|jj%j'j.j/dt*ƒ} | |_$n|jj%j dkrž|j |_$n|j$|_0|jj1j dkrƒ|jj1j2j3}|dkrìt4dƒ‚n+d|kodknst4dƒ‚n|jJ|jd IJ|jd!IJ|jJ|jd"|IJ|j$j5d#|jj1j2j6d$|ƒj7ƒ|_0n½|jj1j d%kr@|jj1j2j6}|jj1j2j3}|dkr×t4d&ƒ‚n+d|koîdknst4dƒ‚n|jd'||fIJ|j$j8d#|d$|ƒj7ƒ|_0n|j0dk sUt‚dS((Ntsilentt remove_anisot miller_arrayt n_residuestn_basesitoutt eigen_minit eigen_meant user_b_isoigtbasics1Non-outliers found by the basic wilson statisticssprotocol will be written out.tp_basic_wilsont return_datatextremes9Non-outliers found by the extreme value wilson statisticstp_extreme_wilsontbeamstops&Outliers found for the beamstop shadows0problems detection protocol will be written out.tleveltd_mintNonettwins.Twin fraction not specified, not twinning datagà?s(Twin fraction must be between 0 and 0.5.sTwinning given datas-------------------s1Artifically twinning the data with fraction %3.2fttwin_lawtalphatdetwins0Twin fraction not specified, not detwinning datas/ Attempting to detwin data ------------------------- Detwinning data with: - twin law: %s - twin fraciton: %.2f BE WARNED! DETWINNING OF DATA DOES NOT SOLVE YOUR TWINNING PROBLEM! PREFERABLY, REFINEMENT SHOULD BE CARRIED OUT AGAINST ORIGINAL DATA ONLY USING A TWIN SPECIFIC TARGET FUNCTION! (9tparamst deep_copytset_observation_typetmerge_equivalentstarrayR RRtsyststdoutRtno_aniso_arraytanisotactionRtml_aniso_absolute_scalingtp_scaletshowt aniso_p_scaletu_start aniso_u_startb_cartt aniso_b_carttfinal_bt eigen_valuesRtmeantb_isotAssertionErrorRtu_cart_as_u_start unit_celltb_as_utanisotropic_correctionRtoutlier_managertnew_miller_arraytoutliertbasic_wilson_outlierst parameterst basic_wilsonRtTruetextreme_wilson_outlierstextreme_wilsontbeamstop_shadow_outliersRRt final_arraytsymmetryttwinning_parameterstfractionRt twin_dataRtas_intensity_arrayt detwin_data(tselfR R?RR Rtaniso_scale_and_btb_usetb_cart_aniso_removedtu_star_aniso_removedR;t basic_arrayt extreme_arraytbeamstop_arrayRR((sT/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/scaling/massage_twin_detwin_data.pyt__init__esÈ                                        cC s|jS(N(RE(RL((sT/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/scaling/massage_twin_detwin_data.pyRòstmassagedc C st|ƒdkrRtjj|ƒ\}}|dkrC|d}qRtdƒ‚n|dksjt|ƒ‚|dkrªddl}|jjj d |d |j d t ƒnq|dkrd}|j j ƒrÔd }n|j jƒrìd }n|j jd||ƒ}|jƒj |ƒndS(NRs.mtzs.scais"Unknown or unsupported output typetmtztscaiÿÿÿÿt file_nameR t%scale_intensities_for_scalepack_mergetItFtcolumn_root_label(s.mtzs.sca(RVRW(tstrtostpathtsplitextRR6tiotbx.scalepack.merget scalepacktmergetwriteRERARtis_xray_intensity_arraytis_xray_amplitude_arraytas_mtz_datasett mtz_object( RLRXt output_typetlabel_extensiontbasetexttiotbxt base_labelt mtz_dataset((sT/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/scaling/massage_twin_detwin_data.pyt write_dataõs*           N(t__name__t __module__RRTRRRp(((sT/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/scaling/massage_twin_detwin_data.pyR ds  ˆ (t __future__Rt mmtbx.scalingRRtmmtbxt iotbx.philRmtcctbx.array_familyRtcctbxRRt libtbx.utilsRRtlibtbxRtos.pathR^R%toutput_params_strtphiltparset master_paramstobjectR (((sT/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/scaling/massage_twin_detwin_data.pyts     J